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 Results for DC.creator="E." AND DC.creator="Gallicchio" in section 18.10.4 of volume F   page 1 of 2 pages.
PrimeX implementation and theory
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4, pp. 536-538 [ doi:10.1107/97809553602060000864 ]
... Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., Felts, A. K., Halgren, T. A. ... P., Zhang, L. Y., Berne, B. J., Friesner, R. A., Gallicchio, E. & Levy, R. M. (2005). Integrated Modeling Program, Applied ...

Ligand placement
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.5, p. 537 [ doi:10.1107/97809553602060000864 ]
... Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P. & Shenkin, P. S. (2004). Glide: a new ...

Water placement
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.4, p. 537 [ doi:10.1107/97809553602060000864 ]
Water placement 18.10.4.4. Water placement Waters may be added by PrimeX to difference electron-density maps for positive peaks exceeding a selected level of significance. Prospective water sites in the electron-density map are screened by three different criteria related to distance from other atoms. Water molecules that refine to a ...

Minimization
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.3, p. 537 [ doi:10.1107/97809553602060000864 ]
Minimization 18.10.4.3.3. Minimization Real-space minimization provides an additional method of optimizing model coordinates according to the electron density and force field, as well as playing an integral part in the building of polypeptide chains, the placement of amino-acid side chains and the placement of ligands. References International Tables for ...

Side-chain placement
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.2, p. 537 [ doi:10.1107/97809553602060000864 ]
Side-chain placement 18.10.4.3.2. Side-chain placement Also based on Prime technology, one or multiple side chains may be simultaneously evaluated and placed into electron density. Even if two side chains have overlapping conformations at the start of the process, they will both be placed into appropriate electron density. As an ...

Loop refinement
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.1, p. 537 [ doi:10.1107/97809553602060000864 ]
... Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E. & Friesner, R. A. (2004). A hierarchical approach to all ...

Real-space tools
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3, p. 537 [ doi:10.1107/97809553602060000864 ]
... Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E. & Friesner, R. A. (2004). A hierarchical approach to all ...

Omit maps
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.4, pp. 536-537 [ doi:10.1107/97809553602060000864 ]
Omit maps 18.10.4.2.4. Omit maps Omit maps (Bhat & Cohen, 1984; Bhat, 1988) have been implemented because of their demonstrated ability to reduce model-derived bias in maps (Vellieux & Dijkstra, 1997). The kicked omit maps described by Guncar et al. (2000) have also been included in PrimeX. After all the atoms ...

Map generation
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.3, p. 536 [ doi:10.1107/97809553602060000864 ]
Map generation 18.10.4.2.3. Map generation Map calculations in PrimeX are based on the sigmaA weighting scheme of Read (1986), a data treatment that has been shown to decrease the bias in electron-density maps. Optionally, an unweighted map may be calculated. References Read, R. J. (1986). Improved Fourier coefficients for ...

Simulated annealing
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.2, p. 536 [ doi:10.1107/97809553602060000864 ]
... Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., Felts, A. K., Halgren, T. A. ... P., Zhang, L. Y., Berne, B. J., Friesner, R. A., Gallicchio, E. & Levy, R. M. (2005). Integrated Modeling Program, Applied ...

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